Introduction

Data from RAB : CD8+ T cells from mice

Report based off of a conversation to tailor the analysis more to Raphaëlle’s needs.

Sample similarity

All violin plots

Nonuc Trpn vs Trpp

Volcano plot

Getting some stats yay

table(res_tbl$padj<=0.05) # significant genes
## 
## FALSE  TRUE 
## 10762  7486
table(res_tbl$padj<=0.05&res_tbl$log2FoldChange<=-1) # signif and downreg
## 
## FALSE  TRUE 
## 21299  2119
table(res_tbl$padj<=0.05&res_tbl$log2FoldChange>=1) # signif and upreg
## 
## FALSE  TRUE 
## 23240   967

GSEA analysis logFc

Summary

ID setSize enrichmentScore NES pvalue p.adjust qvalue
GOBP_RIBOSOME_BIOGENESIS 188 0.4202304 2.264562 0.0000000 0.0000000 NA
GOBP_NCRNA_METABOLIC_PROCESS 291 0.3330353 1.878148 0.0000000 0.0000001 NA
REACTOME_SIRT1_NEGATIVELY_REGULATES_RRNA_EXPRESSION 18 -0.8077241 -2.155432 0.0000005 0.0000029 NA
REACTOME_RESPONSE_OF_EIF2AK1_HRI_TO_HEME_DEFICIENCY 14 0.7983226 2.441334 0.0000061 0.0000274 NA
GOBP_MITOCHONDRIAL_GENE_EXPRESSION 60 0.4937235 2.211376 0.0000079 0.0000284 NA
REACTOME_DNA_METHYLATION 18 -0.7702184 -2.055347 0.0000107 0.0000320 NA
REACTOME_TRANSLATION 150 0.3394148 1.777543 0.0000165 0.0000425 NA
GOBP_MITOCHONDRIAL_TRANSLATION 40 0.5425012 2.215894 0.0000228 0.0000512 NA
REACTOME_MITOCHONDRIAL_TRANSLATION 47 0.5030006 2.139052 0.0000599 0.0001199 NA
HALLMARK_UNFOLDED_PROTEIN_RESPONSE 64 0.4383292 1.971083 0.0000922 0.0001659 NA
REACTOME_CHOLESTEROL_BIOSYNTHESIS 20 -0.6912764 -1.887044 0.0003443 0.0005164 NA
GOBP_INFLAMMATORY_RESPONSE 269 -0.3985508 -1.494997 0.0003190 0.0005164 NA
GOBP_AMINO_ACID_ACTIVATION 26 0.5691117 2.083546 0.0004722 0.0006539 NA
REACTOME_PERK_REGULATES_GENE_EXPRESSION 20 0.6152588 2.090729 0.0006025 0.0007746 NA
HALLMARK_MYC_TARGETS_V1 111 0.3269211 1.618745 0.0007501 0.0009001 NA
REACTOME_OXIDATIVE_STRESS_INDUCED_SENESCENCE 50 -0.5527892 -1.782156 0.0008535 0.0009602 NA
REACTOME_ATF4_ACTIVATES_GENES_IN_RESPONSE_TO_ENDOPLASMIC_RETICULUM_STRESS 17 0.6043709 1.954481 0.0016783 0.0017770 NA
HALLMARK_CHOLESTEROL_HOMEOSTASIS 48 -0.5304719 -1.700395 0.0025638 0.0025638 NA

Get the enrichment plots

Get the enrichment plots for glycolysis and oxphos

Those plots have a non significant adjusted pvalue and a bad qvalue!!

Summary breakdown per function

ORA

Summary

ID GeneRatio p.adjust qvalue
GOBP_STEROL_METABOLIC_PROCESS 48/2195 0.0000846 0.0000754
GOBP_T_CELL_ACTIVATION 103/2195 0.0017908 0.0015966
GOBP_CARBOHYDRATE_CATABOLIC_PROCESS 38/2195 0.0140645 0.0125395
GOBP_POSITIVE_REGULATION_OF_GLYCOLYTIC_PROCESS 10/2195 0.0164616 0.0146767
GOBP_REGULATION_OF_ATP_METABOLIC_PROCESS 25/2195 0.0164616 0.0146767
GOBP_CALCIUM_MEDIATED_SIGNALING 46/2195 0.0208734 0.0186101
GOBP_PYRUVATE_METABOLIC_PROCESS 28/2195 0.0330592 0.0294746
GOBP_CELLULAR_RESPONSE_TO_CALCIUM_ION 23/2195 0.0358732 0.0319835
GOBP_NEGATIVE_REGULATION_OF_LEUKOCYTE_APOPTOTIC_PROCESS 16/2195 0.0415601 0.0370537
GOBP_REGULATION_OF_GLYCOLYTIC_PROCESS 15/2195 0.0439075 0.0391466
GOBP_T_CELL_DIFFERENTIATION 57/2195 0.0456568 0.0407062
GOBP_ADP_METABOLIC_PROCESS 24/2195 0.0456568 0.0407062

Summary breakdown per function

qPCR results found in RNAseq?

ensembl baseMean log2FoldChange padj gene description
ENSMUSG00000006494 3367.734 -1.1100254 0.0000000 Pdk1 pyruvate dehydrogenase kinase, isoenzyme 1 [Source:MGI Symbol;Acc:MGI:1926119]
ENSMUSG00000063229 43943.514 -0.5014518 0.0028179 Ldha lactate dehydrogenase A [Source:MGI Symbol;Acc:MGI:96759]

Heatmap : gene expression per condition

##          Nonuc_Trpn_1 Nonuc_Trpn_2 Nonuc_Trpn_3 Nonuc_Trpp_1 Nonuc_Trpp_2
## Selenbp1   -0.9080445   -0.9848078   -0.8391412    0.8515168    1.0045578
## H2-Q10     -0.8653827   -0.9415914   -0.9297034    0.9125712    0.8690296
## Egln3      -0.9750593   -0.9135665   -0.8447882    0.9555138    0.9502577
## Fads2      -0.8497548   -1.0212553   -0.8557241    1.0241533    0.8982467
## Slc6a9      0.8455653    0.9357059    0.9546301   -0.9522052   -0.9102143
## Gpc1        0.9283341    1.0388258    0.7603420   -0.9118691   -0.8838358
##          Nonuc_Trpp_3
## Selenbp1    0.8759187
## H2-Q10      0.9550767
## Egln3       0.8276425
## Fads2       0.8043342
## Slc6a9     -0.8734818
## Gpc1       -0.9317970

These plots are showing a z-score. If you did the mean(trpn ratio)/mean(trpp ratio), you would get the logFc of the volcano plot

Genes from the ORA results : - GOBP Positive regulation of glycolytic process (10 genes) - GOBP Regulation of ATP metabolic process (25)

Those two terms have most genes in common.

##  [1] "Prxl2c"   "Entpd5"   "Hif1a"    "P2rx7"    "App"      "Mlxipl"  
##  [7] "Htr2a"    "Prkaa2"   "Prkaa1"   "Slc4a4"   "Gapdhs"   "Nupr1"   
## [13] "Prxl2c"   "Shmt2"    "Entpd5"   "Dnajc15"  "Hdac4"    "Sphk2"   
## [19] "Hif1a"    "Slc2a6"   "Trp53"    "Tspo"     "Ak4"      "Slc25a33"
## [25] "Slc25a23" "P2rx7"    "Gck"      "App"      "Mlxipl"   "Cbfa2t3" 
## [31] "Htr2a"    "Cox7a1"   "Prkaa2"   "Pid1"     "Slc4a4"   "Gapdhs"  
## [37] "Atf4"

Heatmap with complete list of glycolysis genes

After a meeting, we wanted to check the expression of a list of more genes more largely implicated in glycolysis. This was also added to the KO analyses. At the end of the document, there are the heatmaps with those genes + OXPHOS and logFc between conditions (and not triplicates with z-scores as in here).

##   [1] "Actn3"    "Adpgk"    "Aldoa"    "Aldoa"    "Aldoa"    "Aldoa"   
##   [7] "Aldoart1" "Aldoart2" "Aldob"    "Aldob"    "Aldob"    "Aldob"   
##  [13] "Aldoc"    "App"      "Arl2"     "Bpgm"     "Cbfa2t3"  "Ddit4"   
##  [19] "Dhtkd1"   "Eif6"     "Eno1"     "Eno1"     "Eno1b"    "Eno1b"   
##  [25] "Eno2"     "Eno2"     "Eno3"     "Eno3"     "Eno3"     "Eno4"    
##  [31] "Eno4"     "Enpp1"    "Ep300"    "Esrrb"    "Fbp1"     "Flcn"    
##  [37] "Foxk1"    "Foxk2"    "Gale"     "Galk1"    "Galk1"    "Galt"    
##  [43] "Galt"     "Gapdh"    "Gapdh"    "Gapdh"    "Gapdh"    "Gapdh"   
##  [49] "Gapdhrt"  "Gapdhrt"  "Gapdhrt2" "Gapdhrt2" "Gapdhs"   "Gapdhs"  
##  [55] "Gapdhs"   "Gapdhs"   "Gck"      "Gck"      "Gck"      "Git1"    
##  [61] "Gpd1"     "Gpi1"     "Gpi1"     "Gpi1"     "Gpi1"     "Gpi1"    
##  [67] "Gpi1"     "Hdac4"    "Hif1a"    "Hif1a"    "Hk1"      "Hk1"     
##  [73] "Hk1"      "Hk1"      "Hk1"      "Hk2"      "Hk3"      "Hkdc1"   
##  [79] "Htr2a"    "Htr2a"    "Ier3"     "Ier3"     "Ifng"     "Igf1"    
##  [85] "Il3"      "Ins1"     "Ins2"     "Insr"     "Jmjd8"    "Kat2b"   
##  [91] "Khk"      "Khk"      "Lipa"     "Mlst8"    "Mlx"      "Mlxipl"  
##  [97] "Mlxipl"   "Mlxipl"   "Mlxipl"   "Mpi"      "Mtch2"    "Mtor"    
## [103] "Myc"      "Myog"     "Ncor1"    "Nupr1"    "Ogdh"     "Ogt"     
## [109] "P2rx7"    "Pfkfb1"   "Pfkfb1"   "Pfkfb1"   "Pfkfb2"   "Pfkl"    
## [115] "Pfkl"     "Pfkl"     "Pfkl"     "Pfkl"     "Pfkl"     "Pfkm"    
## [121] "Pfkm"     "Pfkm"     "Pfkm"     "Pfkm"     "Pfkm"     "Pfkm"    
## [127] "Pfkm"     "Pfkm"     "Pfkm"     "Pfkm"     "Pfkm"     "Pfkm"    
## [133] "Pfkp"     "Pfkp"     "Pfkp"     "Pgam1"    "Pgam1"    "Pgam2"   
## [139] "Pgam2"    "Pgam2"    "Pgk1"     "Pgk1"     "Pgk1"     "Pgk1"    
## [145] "Pgk2"     "Pgk2"     "Pgk2"     "Pklr"     "Pklr"     "Pklr"    
## [151] "Pkm"      "Pkm"      "Pkm"      "Pkm"      "Pkm"      "Pkm"     
## [157] "Ppara"    "Ppargc1a" "Ppp2ca"   "Ppp2ca"   "Prkaa1"   "Prkaa2"  
## [163] "Prkaca"   "Prkaca"   "Prkag2"   "Prkag3"   "Prxl2c"   "Psen1"   
## [169] "Rptor"    "Sik2"     "Sirt6"    "Sirt6"    "Sirt6"    "Slc2a6"  
## [175] "Slc2a6"   "Slc4a1"   "Slc4a4"   "Slc4a4"   "Stat3"    "Tigar"   
## [181] "Tigar"    "Tigar"    "Tkfc"     "Tpi1"     "Tpi1"     "Tpi1"    
## [187] "Trex1"    "Ucp2"     "Zbtb7a"   "Zbtb20"

Trpp Mrpl28 KO vs scramble

Volcano plot

Getting some stats yay

table(res_tbl$padj<=0.05) # significant genes
## 
## FALSE  TRUE 
## 10762  7486
table(res_tbl$padj<=0.05&res_tbl$log2FoldChange<=-1) # signif and downreg
## 
## FALSE  TRUE 
## 21299  2119
table(res_tbl$padj<=0.05&res_tbl$log2FoldChange>=1) # signif and upreg
## 
## FALSE  TRUE 
## 23240   967

GSEA analysis logFc

Nous n’inclurons pas l’analyse GSEA pour les Mrpl28 KO Trpp parce que les p-valeurs ne sont pas intéressantes.

ORA

Summary

ID GeneRatio p.adjust qvalue
GOBP_RESPONSE_TO_OXYGEN_LEVELS 15/149 0.0005004 0.0004535
GOBP_GENERATION_OF_PRECURSOR_METABOLITES_AND_ENERGY 18/149 0.0006691 0.0006064
GOBP_CELLULAR_RESPONSE_TO_OXYGEN_LEVELS 10/149 0.0008611 0.0007804
GOBP_ADP_METABOLIC_PROCESS 8/149 0.0008611 0.0007804
GOBP_PYRUVATE_METABOLIC_PROCESS 8/149 0.0018691 0.0016941
GOBP_CARBOHYDRATE_CATABOLIC_PROCESS 8/149 0.0135657 0.0122953
GOBP_ATP_METABOLIC_PROCESS 10/149 0.0287394 0.0260479

Heatmap : gene expression per condition

##          Mrpl_Trpp_1 Mrpl_Trpp_2 Mrpl_Trpp_3 Scr_Trpp_1 Scr_Trpp_2 Scr_Trpp_3
## Lrp1      -0.8259607  -0.9569098  -0.8002535  0.2935852  1.3098769  0.9796618
## Ifi203     0.5387867   1.3350253   0.7647435 -0.8184582 -1.0004168 -0.8196805
## Smtnl2    -0.6877219  -0.9613148  -0.8100861  0.1115141  1.4726389  0.8749698
## Tgm2      -0.6187373  -1.1524911  -0.8941781  1.1695848  0.7846807  0.7111410
## Hilpda    -0.5133069  -1.0617170  -0.9732520  0.3955490  1.3833473  0.7693795
## Tmem106a  -0.6176510  -1.1095019  -0.7485602  0.2855056  0.6784788  1.5117287
## [1] "Me1 Nos2 Cox6a2 Bnip3 Ak4 mt-Nd2 Pgm1 P4ha2 Gys1 Gipr Gck Nupr1 Pgam1 Aldoc Pygl Slc4a4 Pfkl Gbe1"
## [1] "Cox6a2 Ak4 mt-Nd2 Pgm1 Gck Nupr1 Pgam1 Aldoc Slc4a4 Pfkl"

All genes implicated in ATP metabolism, precursor generation and response to oxygen are the same ones.

Heatmap with complete list of glycolysis genes

##   [1] "Actn3"    "Adpgk"    "Aldoa"    "Aldoa"    "Aldoa"    "Aldoa"   
##   [7] "Aldoart1" "Aldoart2" "Aldob"    "Aldob"    "Aldob"    "Aldob"   
##  [13] "Aldoc"    "App"      "Arl2"     "Bpgm"     "Cbfa2t3"  "Ddit4"   
##  [19] "Dhtkd1"   "Eif6"     "Eno1"     "Eno1"     "Eno1b"    "Eno1b"   
##  [25] "Eno2"     "Eno2"     "Eno3"     "Eno3"     "Eno3"     "Eno4"    
##  [31] "Eno4"     "Enpp1"    "Ep300"    "Esrrb"    "Fbp1"     "Flcn"    
##  [37] "Foxk1"    "Foxk2"    "Gale"     "Galk1"    "Galk1"    "Galt"    
##  [43] "Galt"     "Gapdh"    "Gapdh"    "Gapdh"    "Gapdh"    "Gapdh"   
##  [49] "Gapdhrt"  "Gapdhrt"  "Gapdhrt2" "Gapdhrt2" "Gapdhs"   "Gapdhs"  
##  [55] "Gapdhs"   "Gapdhs"   "Gck"      "Gck"      "Gck"      "Git1"    
##  [61] "Gpd1"     "Gpi1"     "Gpi1"     "Gpi1"     "Gpi1"     "Gpi1"    
##  [67] "Gpi1"     "Hdac4"    "Hif1a"    "Hif1a"    "Hk1"      "Hk1"     
##  [73] "Hk1"      "Hk1"      "Hk1"      "Hk2"      "Hk3"      "Hkdc1"   
##  [79] "Htr2a"    "Htr2a"    "Ier3"     "Ier3"     "Ifng"     "Igf1"    
##  [85] "Il3"      "Ins1"     "Ins2"     "Insr"     "Jmjd8"    "Kat2b"   
##  [91] "Khk"      "Khk"      "Lipa"     "Mlst8"    "Mlx"      "Mlxipl"  
##  [97] "Mlxipl"   "Mlxipl"   "Mlxipl"   "Mpi"      "Mtch2"    "Mtor"    
## [103] "Myc"      "Myog"     "Ncor1"    "Nupr1"    "Ogdh"     "Ogt"     
## [109] "P2rx7"    "Pfkfb1"   "Pfkfb1"   "Pfkfb1"   "Pfkfb2"   "Pfkl"    
## [115] "Pfkl"     "Pfkl"     "Pfkl"     "Pfkl"     "Pfkl"     "Pfkm"    
## [121] "Pfkm"     "Pfkm"     "Pfkm"     "Pfkm"     "Pfkm"     "Pfkm"    
## [127] "Pfkm"     "Pfkm"     "Pfkm"     "Pfkm"     "Pfkm"     "Pfkm"    
## [133] "Pfkp"     "Pfkp"     "Pfkp"     "Pgam1"    "Pgam1"    "Pgam2"   
## [139] "Pgam2"    "Pgam2"    "Pgk1"     "Pgk1"     "Pgk1"     "Pgk1"    
## [145] "Pgk2"     "Pgk2"     "Pgk2"     "Pklr"     "Pklr"     "Pklr"    
## [151] "Pkm"      "Pkm"      "Pkm"      "Pkm"      "Pkm"      "Pkm"     
## [157] "Ppara"    "Ppargc1a" "Ppp2ca"   "Ppp2ca"   "Prkaa1"   "Prkaa2"  
## [163] "Prkaca"   "Prkaca"   "Prkag2"   "Prkag3"   "Prxl2c"   "Psen1"   
## [169] "Rptor"    "Sik2"     "Sirt6"    "Sirt6"    "Sirt6"    "Slc2a6"  
## [175] "Slc2a6"   "Slc4a1"   "Slc4a4"   "Slc4a4"   "Stat3"    "Tigar"   
## [181] "Tigar"    "Tigar"    "Tkfc"     "Tpi1"     "Tpi1"     "Tpi1"    
## [187] "Trex1"    "Ucp2"     "Zbtb7a"   "Zbtb20"

Trpp Ndufa2 KO vs scramble

Volcano plot

Getting some stats yay

table(res_tbl$padj<=0.05) # significant genes
## 
## FALSE  TRUE 
## 10762  7486
table(res_tbl$padj<=0.05&res_tbl$log2FoldChange<=-1) # signif and downreg
## 
## FALSE  TRUE 
## 21299  2119
table(res_tbl$padj<=0.05&res_tbl$log2FoldChange>=1) # signif and upreg
## 
## FALSE  TRUE 
## 23240   967

GSEA analysis logFc

Nous n’inclurons pas l’analyse GSEA pour les Ndufa2 KO Trpp parce que les p-valeurs ne sont pas intéressantes.

ORA

Summary

ID GeneRatio p.adjust qvalue
HALLMARK_HYPOXIA 36/256 0.0000000 0.0000000
HALLMARK_GLYCOLYSIS 23/256 0.0000000 0.0000000
WP_GLYCOLYSIS_AND_GLUCONEOGENESIS 13/256 0.0000000 0.0000000
GOBP_ADP_METABOLIC_PROCESS 15/256 0.0000000 0.0000000
GOBP_PYRUVATE_METABOLIC_PROCESS 15/256 0.0000000 0.0000000
GOBP_GENERATION_OF_PRECURSOR_METABOLITES_AND_ENERGY 30/256 0.0000000 0.0000000
WP_AEROBIC_GLYCOLYSIS 7/256 0.0000001 0.0000001
REACTOME_METABOLISM_OF_CARBOHYDRATES 22/256 0.0000002 0.0000002
GOBP_CARBOHYDRATE_CATABOLIC_PROCESS 16/256 0.0000004 0.0000003
GOBP_RESPONSE_TO_OXYGEN_LEVELS 21/256 0.0000039 0.0000034
GOBP_CELLULAR_RESPONSE_TO_OXYGEN_LEVELS 14/256 0.0000249 0.0000221
REACTOME_GLYCOLYSIS 10/256 0.0000250 0.0000221
REACTOME_GLUCOSE_METABOLISM 10/256 0.0002238 0.0001984
GOBP_NAD_METABOLIC_PROCESS 6/256 0.0005858 0.0005192
GOBP_ATP_METABOLIC_PROCESS 16/256 0.0006022 0.0005337
GOBP_NADH_REGENERATION 4/256 0.0020365 0.0018049
GOBP_GLYCOLYTIC_PROCESS_THROUGH_FRUCTOSE_6_PHOSPHATE 4/256 0.0052891 0.0046875
GOBP_NADH_METABOLIC_PROCESS 5/256 0.0078645 0.0069699
GOBP_GLUCOSE_CATABOLIC_PROCESS 4/256 0.0138548 0.0122789

Heatmap : gene expression per condition

##          Nduf_Trpp_1 Nduf_Trpp_2 Nduf_Trpp_3 Scr_Trpp_1 Scr_Trpp_2 Scr_Trpp_3
## Fam183b   -0.9148785  -1.0100591  -0.8009006  0.8831629   1.030043  0.8126325
## Itga7     -0.8730611  -0.8660348  -0.8612939  0.2942344   1.162318  1.1438372
## Selenbp1  -0.7857927  -0.9752700  -0.9431417  0.6758335   1.132437  0.8959336
## Gbe1      -0.6986521  -1.0620895  -0.9423754  0.7208727   1.066871  0.9153732
## Fam162a   -0.8109325  -1.0705502  -0.8227344  0.7521822   1.131614  0.8204207
## Grin1     -0.8828204  -0.9534518  -0.8352825  0.4964621   1.056948  1.1181444
## [1] "Gbe1 Gipr Me1 Loxl2 Aldoc Bnip3 Nos2 Pgk1 Pgm1 Tpi1 Pgam1 Pkm Gapdh Gck Ak4 P4ha2 Hk2 Gys1 Ppp1r3g Xylb Pfkl Slc4a4 P2rx7 Eno1 Pygl Ldha Il6st Prdm16 Cavin3 Cox4i2"
## [1] "Cox6a2 Ak4 mt-Nd2 Pgm1 Gck Nupr1 Pgam1 Aldoc Slc4a4 Pfkl"

Heatmap with complete list of glycolysis genes

##   [1] "Actn3"    "Adpgk"    "Aldoa"    "Aldoa"    "Aldoa"    "Aldoa"   
##   [7] "Aldoart1" "Aldoart2" "Aldob"    "Aldob"    "Aldob"    "Aldob"   
##  [13] "Aldoc"    "App"      "Arl2"     "Bpgm"     "Cbfa2t3"  "Ddit4"   
##  [19] "Dhtkd1"   "Eif6"     "Eno1"     "Eno1"     "Eno1b"    "Eno1b"   
##  [25] "Eno2"     "Eno2"     "Eno3"     "Eno3"     "Eno3"     "Eno4"    
##  [31] "Eno4"     "Enpp1"    "Ep300"    "Esrrb"    "Fbp1"     "Flcn"    
##  [37] "Foxk1"    "Foxk2"    "Gale"     "Galk1"    "Galk1"    "Galt"    
##  [43] "Galt"     "Gapdh"    "Gapdh"    "Gapdh"    "Gapdh"    "Gapdh"   
##  [49] "Gapdhrt"  "Gapdhrt"  "Gapdhrt2" "Gapdhrt2" "Gapdhs"   "Gapdhs"  
##  [55] "Gapdhs"   "Gapdhs"   "Gck"      "Gck"      "Gck"      "Git1"    
##  [61] "Gpd1"     "Gpi1"     "Gpi1"     "Gpi1"     "Gpi1"     "Gpi1"    
##  [67] "Gpi1"     "Hdac4"    "Hif1a"    "Hif1a"    "Hk1"      "Hk1"     
##  [73] "Hk1"      "Hk1"      "Hk1"      "Hk2"      "Hk3"      "Hkdc1"   
##  [79] "Htr2a"    "Htr2a"    "Ier3"     "Ier3"     "Ifng"     "Igf1"    
##  [85] "Il3"      "Ins1"     "Ins2"     "Insr"     "Jmjd8"    "Kat2b"   
##  [91] "Khk"      "Khk"      "Lipa"     "Mlst8"    "Mlx"      "Mlxipl"  
##  [97] "Mlxipl"   "Mlxipl"   "Mlxipl"   "Mpi"      "Mtch2"    "Mtor"    
## [103] "Myc"      "Myog"     "Ncor1"    "Nupr1"    "Ogdh"     "Ogt"     
## [109] "P2rx7"    "Pfkfb1"   "Pfkfb1"   "Pfkfb1"   "Pfkfb2"   "Pfkl"    
## [115] "Pfkl"     "Pfkl"     "Pfkl"     "Pfkl"     "Pfkl"     "Pfkm"    
## [121] "Pfkm"     "Pfkm"     "Pfkm"     "Pfkm"     "Pfkm"     "Pfkm"    
## [127] "Pfkm"     "Pfkm"     "Pfkm"     "Pfkm"     "Pfkm"     "Pfkm"    
## [133] "Pfkp"     "Pfkp"     "Pfkp"     "Pgam1"    "Pgam1"    "Pgam2"   
## [139] "Pgam2"    "Pgam2"    "Pgk1"     "Pgk1"     "Pgk1"     "Pgk1"    
## [145] "Pgk2"     "Pgk2"     "Pgk2"     "Pklr"     "Pklr"     "Pklr"    
## [151] "Pkm"      "Pkm"      "Pkm"      "Pkm"      "Pkm"      "Pkm"     
## [157] "Ppara"    "Ppargc1a" "Ppp2ca"   "Ppp2ca"   "Prkaa1"   "Prkaa2"  
## [163] "Prkaca"   "Prkaca"   "Prkag2"   "Prkag3"   "Prxl2c"   "Psen1"   
## [169] "Rptor"    "Sik2"     "Sirt6"    "Sirt6"    "Sirt6"    "Slc2a6"  
## [175] "Slc2a6"   "Slc4a1"   "Slc4a4"   "Slc4a4"   "Stat3"    "Tigar"   
## [181] "Tigar"    "Tigar"    "Tkfc"     "Tpi1"     "Tpi1"     "Tpi1"    
## [187] "Trex1"    "Ucp2"     "Zbtb7a"   "Zbtb20"

Summary heatmap for oxphos and glycolysis

OXPHOS

Trp+ vs Trp-

NAs replaced by 0s

Nonuc and KOs vs scramble in Trp+ or Trp-

Glycolysis

Trp+ vs Trp-

NAs replaced by 0s

Nonuc and KOs vs scramble in Trp+ or Trp-